A network-based approach to identify substrate classes of bacterial glycosyltransferases

Sánchez-Rodríguez, Aminael; Tytgat, Hanne LP; Winderickx, Joris; Vanderleyden, Jos; Lebeer, Sarah; Marchal, Kathleen

doi:10.1186/1471-2164-15-349

BMC Genomics

Table 2 Updated annotation of glycosyltransferases predicted in the genome of Lactobacillus rhamnosus GG

From: A network-based approach to identify substrate classes of bacterial glycosyltransferases

Locus tag	Current annotation	Proposed annotation	HMM	Evidence	Reference
LGG_00279	welA; dTDP-rhamnosyl transferase rfbF	wclA; glycosyltransferase (putative cell wall polysaccharide biosynthesis)	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00280	welB; alpha-L-Rha alpha-1,3-L-rhamnosyltransferase	wclB; glycosyltransferase (putative cell wall polysaccharide biosynthesis)	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00281	welC; alpha-L-Rha alpha-1,3-L-rhamnosyltransferase	wclC; glycosyltransferase (putative cell wall polysaccharide biosynthesis)	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00283*	eps2; hypothetical protein	wclD; putative glycosyltransferase (putative cell wall polysaccharide biosynthesis)	UDP-Glycosyltransferase	-	-
LGG_00295	Glycosyltransferase, group 2	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00348	yohJ; lipopolysaccharide biosynthesis protein	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_00349	yohH; polyglycerol-phosphate alpha-glucosyltransferase	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_00645	Glycosyltransferase, group 2	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00695	gtrB; glycosyltransferase, group 2	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00794	pbp1B; penicillin-binding protein 1B	pbpb1B; putative glycosyltransferase, penicillin-binding protein 1B (peptidoglycan biosynthesis)	Pfam/CAZy	Conservation	Kankainen et al., 2009 [44]
LGG_00825	rfaG; glycosyltransferase, group 1	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_00826	cpoA; glycosyltransferase, group 1	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_00928*	yvcK; transporter	Putative glycosyltransferase	Rossmann-fold domains	-	-
LGG_00985*	Integral membrane protein	Putative glycosyltransferase	Pfam/CAZy	-	-
LGG_00998	arbX; lipopolysaccharide biosynthesis glycosyltransferase	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_00999	arbY; lipopolysaccharide biosynthesis glycosyltransferase	Putative glycosyltransferase	Rossmann-fold domains	Conservation	Kankainen et al., 2009 [44]
LGG_01057	Glycosyltransferase, group 2	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_01062^#	galU; UTP-glucose-1-phosphate uridylyltransferase	UTP-glucose-1-phosphate uridylyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_01069	gtrB; glycosyltransferase, group 2	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_01147	Glycosyltransferase, group 1	Putative glycosyltransferase	Rossmann-fold domains	Conservation	Kankainen et al., 2009 [44]
LGG_01195*	metQ; ABC transporter	ABC transporter, putative bifunctional glycosyltransferase	Pfam	-	-
LGG_01283	murG; undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase	murG; undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase (peptidoglycan biosynthesis)	UDP-Glycosyltransferase	Conservation	Mengin-Lecreulx et al., 1991 [26]; Kankainen et al., 2009 [44]
LGG_01412*	trmFO; tRNA uracil-5-methyltransferase	tRNA uracil −5-methyltransferase, putative bifunctional glycosyltransferase	Rossmann-fold domains	-	-
LGG_01487	pbp1A; penicillin-binding protein 1A	pbp1A; putative glycosyltransferase, penicillin-binding protein 1A (peptidoglycan biosynthesis)	Pfam/CAZy	Conservation	Kankainen et al., 2009 [44]
LGG_01538	Phage-related glycosyltransferase	Putative glycosyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_01586	yohH; glycosyltransferase, group 1	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_01587	yohJ; glycosyltransferase, group 1	Putative glycosyltransferase	Rossmann-fold domains	Conservation	Kankainen et al., 2009 [44]
LGG_01783	pbp2A; membrane carboxypeptidase, penicillin-binding protein 2A	pbp2A; bifunctional membrane carboxypeptidase, putative glycosyltransferase, penicillin-binding protein 2A (peptidoglycan biosynthesis)	Pfam/CAZy	Conservation	Di Guilmi et al., 2003 [17]; Kankainen et al., 2009 [44]
LGG_01991*	UDP-N-acetylglucosamine 2-epimerase	Epimerase, putative bifunctional glycosyltransferase	UDP-Glycosyltransferase	-	-
LGG_01992*	UDP-N-acetylglucosamine 2-epimerase	Epimerase, putative bifunctional glycosyltransferase	Sugar transferase	-	-
LGG_01999	rmlA; glucose-1-phosphate thymidylyltransferase	rmlA; glucose-1-phosphate thymidylyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_02004	eps3; sugar or lipopolysaccharide synthesis transferase	Putative glycosyltransferase	Pfam	Conservation	Kankainen et al., 2009 [44]
LGG_02023^#	glgP; glycogen starch alpha-glucan phosphorylase	glgP, glycogen alpha-glucan phosphorylase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_02024	glgA; glycogen synthase	glgA; glycogen synthase (glycogen biosynthesis)	UDP-Glycosyltransferase	Conservation	Kiel et al., 1994 [42]; Kankainen et al., 2009 [44]
LGG_02025^#	glgD; glucose-1-phosphate adenylyltransferase	glgD; glucose-1-phosphate adenylyltransferase (glycogen biosynthesis)	Sugar transferase	Conservation	Ballicora et al., 2003 [56]; Kankainen et al., 2009 [44]
LGG_02026^#	glgC; glucose-1-phosphate adenylyltransferase	glgC; glucose-1-phosphate adenylyltransferase (glycogen biosynthesis)	Sugar transferase	Conservation	Ballicora et al., 2003 [56]; Kankainen et al., 2009 [44]
LGG_02040^$	rmlA1; glucose-1-phosphate thymidyl transferase	rmlA1; glucose-1-phosphate thymidyl transferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_02042	rmlA2; glucose-1-phosphate thymidylyltransferase	rmlA2; glucose-1-phosphate thymidylyltransferase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_02043	welE; undecaprenyl-phosphate beta-glucosephosphotransferase	welE; priming glycosyltransferase (galactose-rich EPS biosynthesis)	Pfam	Experimental validation	Lebeer et al., 2009 [37]
LGG_02044	welF; glycosyltransferase, group 1	welF; putative glycosyltransferase (galactose-rich EPS biosynthesis)	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_02045	welG; glycosyltransferase, galactofuranosyltransferase	welG; putative glycosyltransferase (galactose-rich EPS biosynthesis)	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_02046	welH; alpha-L-Rha alpha-1,3-L-rhamnosyltransferase	welH; putative glycoysltransferase (galactose-rich EPS biosynthesis)	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_02047	welI; glycosyltransferase, group 1	welI; glycosyltransferase (galactose-rich EPS biosynthesis)	UDP-Glycosyltransferase	Experimental validation	This work
LGG_02284	Glycosyltransferase, group 1	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_02285	yohH; glycosyltransferase, group 1	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]
LGG_02347*	Hypothetical protein	Putative glycosyltransferase	Pfam	-	-
LGG_02562^#	glmU; UDP-N-acetylglucosamine pyrophosphorylase	UDP-N-acetylglucosamine pyrophosphorylase	Sugar transferase	Conservation	Kankainen et al., 2009 [44]
LGG_02869	Glycosyltransferase, group 1	Putative glycosyltransferase	UDP-Glycosyltransferase	Conservation	Kankainen et al., 2009 [44]

Locus tag: gene identifier of the predicted GT. Genes for which a GT activity was predicted in this study that was not present in the current annotation are marked with a star (*). Potential false positive results are indicated with a hash (^#). Current annotation: functional annotation as in current genome release of GenBank (NC_013198.1). Proposed annotation: new annotation proposed based on the results of our analysis. HMM: description of the Hidden Markov Model (HMM) with which the indicated GT was identified. Evidence: Level of evidence for the GT activity. Conservation: shows significant sequence conservation with an experimentally validated GT in a closely related species. Experimental validation: the GT activity has been experimentally validated in Lactobacillus rhamnosus GG. Reference: reference to the publication(s) supporting the evidence.

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ISSN: 1471-2164

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